####################################################### # # # LGA # # --------------- # # # # Local-Global Alignment # # A Method for Finding 3-D Similarities # # in Protein Structures # # # # ------------ 09/2011 # # # # Adam Zemla (adamz@llnl.gov) # # Lawrence Livermore National Laboratory, CA # # # ####################################################### # Molecule1: number of CA atoms 21 ( 157), selected 21 , name T0970TS347_4 # Molecule2: number of CA atoms 85 ( 650), selected 21 , name T0970.pdb # PARAMETERS: -3 -ie -o1 -sda -d:4 -gdc_sc -swap T0970TS347_4.lga # FIXED Atom-Atom correspondence # GDT and LCS analysis LCS - RMSD CUTOFF 5.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 21 55 - 75 1.76 1.76 LCS_AVERAGE: 24.71 LCS - RMSD CUTOFF 2.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 21 55 - 75 1.76 1.76 LCS_AVERAGE: 24.71 LCS - RMSD CUTOFF 1.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 15 55 - 69 0.77 1.89 LCS_AVERAGE: 15.57 LCS_GDT MOLECULE-1 MOLECULE-2 LCS_DETAILS GDT_DETAILS TOTAL NUMBER OF RESIDUE PAIRS: 21 LCS_GDT RESIDUE RESIDUE SEGMENT_SIZE GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair LCS_GDT NAME NUMBER NAME NUMBER 1.0 2.0 5.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0 8.5 9.0 9.5 10.0 LCS_GDT E 55 E 55 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT Q 56 Q 56 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT A 57 A 57 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT F 58 F 58 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT D 59 D 59 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT R 60 R 60 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT L 61 L 61 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT S 62 S 62 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT E 63 E 63 15 21 21 9 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT A 64 A 64 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT G 65 G 65 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT F 66 F 66 15 21 21 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT H 67 H 67 15 21 21 8 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT M 68 M 68 15 21 21 6 10 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT V 69 V 69 15 21 21 6 11 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT A 70 A 70 13 21 21 4 5 8 15 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT C 71 C 71 13 21 21 4 11 16 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT N 72 N 72 13 21 21 4 12 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT S 73 S 73 6 21 21 4 5 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT S 74 S 74 5 21 21 3 14 16 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT G 75 G 75 3 21 21 3 3 4 6 7 7 10 20 21 21 21 21 21 21 21 21 21 21 21 21 LCS_AVERAGE LCS_A: 21.66 ( 15.57 24.71 24.71 ) GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds) GDT DIST_CUTOFF 0.50 1.00 1.50 2.00 2.50 3.00 3.50 4.00 4.50 5.00 5.50 6.00 6.50 7.00 7.50 8.00 8.50 9.00 9.50 10.00 GDT NUMBER_AT 11 14 17 18 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 GDT PERCENT_AT 12.94 16.47 20.00 21.18 22.35 23.53 23.53 23.53 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 GDT RMS_LOCAL 0.37 0.50 0.86 0.95 1.06 1.28 1.28 1.28 1.76 1.76 1.76 1.76 1.76 1.76 1.76 1.76 1.76 1.76 1.76 1.76 GDT RMS_ALL_AT 2.45 2.01 1.87 1.82 1.85 1.88 1.88 1.88 1.76 1.76 1.76 1.76 1.76 1.76 1.76 1.76 1.76 1.76 1.76 1.76 # Checking swapping # possible swapping detected: F 58 F 58 # Molecule1 Molecule2 DISTANCE Mis MC All Dist_max GDC_mc GDC_all Dist_at LGA E 55 E 55 1.527 0 0.084 1.280 5.687 58.182 34.747 5.687 LGA Q 56 Q 56 1.065 0 0.028 0.618 2.064 73.636 62.828 1.261 LGA A 57 A 57 0.325 0 0.050 0.055 0.552 95.455 96.364 - LGA F 58 F 58 1.026 0 0.012 0.281 2.395 77.727 56.033 2.367 LGA D 59 D 59 1.010 0 0.035 0.114 1.742 77.727 66.136 1.742 LGA R 60 R 60 0.765 0 0.022 1.013 4.473 81.818 55.372 4.473 LGA L 61 L 61 0.546 0 0.011 0.091 0.845 86.364 84.091 0.599 LGA S 62 S 62 0.574 0 0.022 0.596 2.127 81.818 74.545 2.127 LGA E 63 E 63 0.373 0 0.089 0.203 0.986 100.000 91.919 0.799 LGA A 64 A 64 0.583 0 0.116 0.125 1.025 77.727 78.545 - LGA G 65 G 65 0.108 0 0.089 0.089 0.343 100.000 100.000 - LGA F 66 F 66 0.699 0 0.032 0.166 1.344 81.818 77.355 1.234 LGA H 67 H 67 0.692 0 0.172 1.270 6.138 86.364 49.818 6.138 LGA M 68 M 68 1.527 0 0.037 1.246 6.457 58.182 34.545 5.630 LGA V 69 V 69 0.976 0 0.022 0.075 2.347 63.182 56.104 2.323 LGA A 70 A 70 3.197 0 0.000 0.002 4.595 47.273 38.182 - LGA C 71 C 71 1.884 0 0.059 0.810 3.362 41.818 35.455 3.362 LGA N 72 N 72 1.146 0 0.109 0.222 2.329 77.727 59.545 2.225 LGA S 73 S 73 1.183 0 0.048 0.576 3.696 65.909 52.121 3.696 LGA S 74 S 74 2.175 0 0.079 0.581 3.888 29.545 36.970 2.185 LGA G 75 G 75 6.406 0 0.497 0.497 6.460 0.455 0.455 - # RMSD_GDC results: CA MC common percent ALL common percent GDC_mc GDC_all GDC_at NUMBER_OF_ATOMS_AA: 21 84 84 100.00 156 156 100.00 85 16 SUMMARY(RMSD_GDC): 1.756 1.652 2.149 17.209 14.602 35.682 #CA N1 N2 DIST N RMSD GDT_TS LGA_S3 LGA_Q SUMMARY(GDT) 21 85 4.0 20 1.28 21.471 23.101 1.448 LGA_LOCAL RMSD: 1.281 Number of atoms: 20 under DIST: 4.00 LGA_ASGN_ATOMS RMSD: 1.875 Number of assigned atoms: 21 Std_ASGN_ATOMS RMSD: 1.756 Standard rmsd on all 21 assigned CA atoms Unitary ROTATION matrix and the SHIFT vector superimpose molecules (1=>2) X_new = 0.802784 * X + -0.408884 * Y + 0.433996 * Z + 5.659357 Y_new = -0.591000 * X + -0.642189 * Y + 0.488173 * Z + 78.936615 Z_new = 0.079101 * X + -0.648388 * Y + -0.757189 * Z + 85.810486 Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ: Phi Theta Psi [DEG: Phi Theta Psi ] XYZ: -0.634603 -0.079184 -2.433447 [DEG: -36.3601 -4.5369 -139.4262 ] ZXZ: 2.414877 2.429796 3.020195 [DEG: 138.3622 139.2170 173.0444 ] # END of job REMARK ---------------------------------------------------------- REMARK Citing LGA: REMARK Zemla A., LGA - a Method for Finding 3D Similarities in REMARK Protein Structures, Nucleic Acids Research, 2003, V. 31, REMARK No. 13, pp. 3370-3374. REMARK ---------------------------------------------------------- REMARK Superimposed MOLECULES (1=>2) Output: 1 molecule REMARK 1: T0970TS347_4 REMARK 2: T0970.pdb REMARK GDT and LCS analysis REMARK FIXED Atom-Atom correspondence REMARK LGA parameters: -3 -ie -o1 -sda -d:4 -gdc_sc -swap T0970TS347_4.lga REMARK #CA N1 N2 DIST N RMSD LGA_S3 RMSD_global REMARK SUMMARY: 21 85 4.0 20 1.28 23.101 1.76 REMARK ---------------------------------------------------------- MOLECULE T0970TS347_4 PFRMAT TS TARGET T0970 MODEL 4 PARENT 1wpl_R 1jg5_B ATOM 1 N GLU 55 64.935 38.165 95.471 1.00 3.00 ATOM 0 CA GLU 55 66.384 38.440 95.400 1.00 3.00 ATOM 2 CB GLU 55 66.892 39.011 96.727 1.00 3.00 ATOM 3 C GLU 55 67.154 37.169 95.055 1.00 3.00 ATOM 4 O GLU 55 67.964 37.160 94.125 1.00 3.00 ATOM 5 CG GLU 55 68.407 39.132 96.805 1.00 3.00 ATOM 6 CD GLU 55 68.898 39.616 98.159 1.00 3.00 ATOM 7 OE1 GLU 55 68.150 39.477 99.153 1.00 3.00 ATOM 8 OE2 GLU 55 70.035 40.134 98.233 1.00 3.00 ATOM 10 N GLN 56 66.898 36.094 95.793 1.00 2.12 ATOM 9 CA GLN 56 67.593 34.832 95.560 1.00 2.12 ATOM 12 CB GLN 56 67.179 33.795 96.608 1.00 2.12 ATOM 13 C GLN 56 67.303 34.300 94.162 1.00 2.12 ATOM 14 O GLN 56 68.212 33.848 93.463 1.00 2.12 ATOM 15 CG GLN 56 68.010 32.521 96.575 1.00 2.12 ATOM 16 CD GLN 56 67.784 31.645 97.793 1.00 2.12 ATOM 17 NE2 GLN 56 68.835 30.969 98.244 1.00 2.12 ATOM 20 OE1 GLN 56 66.675 31.583 98.332 1.00 2.12 ATOM 22 N ALA 57 66.037 34.342 93.758 1.00 2.11 ATOM 21 CA ALA 57 65.658 33.897 92.420 1.00 2.11 ATOM 24 CB ALA 57 64.174 34.164 92.184 1.00 2.11 ATOM 25 C ALA 57 66.483 34.642 91.377 1.00 2.11 ATOM 26 O ALA 57 66.998 34.042 90.430 1.00 2.11 ATOM 28 N PHE 58 66.628 35.949 91.572 1.00 1.45 ATOM 27 CA PHE 58 67.368 36.783 90.633 1.00 1.45 ATOM 30 CB PHE 58 67.044 38.265 90.860 1.00 1.45 ATOM 31 C PHE 58 68.869 36.537 90.737 1.00 1.45 ATOM 32 O PHE 58 69.568 36.516 89.722 1.00 1.45 ATOM 33 CG PHE 58 65.595 38.593 90.615 1.00 1.45 ATOM 34 CD1 PHE 58 64.882 39.336 91.549 1.00 1.45 ATOM 35 CE1 PHE 58 63.547 39.656 91.312 1.00 1.45 ATOM 36 CZ PHE 58 62.934 39.247 90.135 1.00 1.45 ATOM 37 CD2 PHE 58 64.962 38.134 89.466 1.00 1.45 ATOM 38 CE2 PHE 58 63.627 38.453 89.232 1.00 1.45 ATOM 40 N ASP 59 69.369 36.354 91.954 1.00 1.24 ATOM 39 CA ASP 59 70.785 36.064 92.146 1.00 1.24 ATOM 42 CB ASP 59 71.116 35.942 93.637 1.00 1.24 ATOM 43 C ASP 59 71.140 34.770 91.420 1.00 1.24 ATOM 44 O ASP 59 72.215 34.652 90.828 1.00 1.24 ATOM 45 CG ASP 59 71.191 37.287 94.337 1.00 1.24 ATOM 46 OD1 ASP 59 71.395 38.310 93.649 1.00 1.24 ATOM 47 OD2 ASP 59 71.038 37.328 95.577 1.00 1.24 ATOM 49 N ARG 60 70.221 33.809 91.448 1.00 1.50 ATOM 48 CA ARG 60 70.413 32.541 90.755 1.00 1.50 ATOM 51 CB ARG 60 69.325 31.542 91.157 1.00 1.50 ATOM 52 C ARG 60 70.384 32.759 89.246 1.00 1.50 ATOM 53 O ARG 60 71.192 32.185 88.513 1.00 1.50 ATOM 54 CG ARG 60 69.477 31.008 92.574 1.00 1.50 ATOM 55 CD ARG 60 68.201 30.333 93.058 1.00 1.50 ATOM 56 NE ARG 60 68.386 29.695 94.358 1.00 1.50 ATOM 58 CZ ARG 60 67.408 29.186 95.101 1.00 1.50 ATOM 59 NH1 ARG 60 67.682 28.625 96.274 1.00 1.50 ATOM 60 NH2 ARG 60 66.149 29.245 94.679 1.00 1.50 ATOM 62 N LEU 61 69.466 33.603 88.786 1.00 1.00 ATOM 61 CA LEU 61 69.361 33.919 87.365 1.00 1.00 ATOM 64 CB LEU 61 68.168 34.848 87.115 1.00 1.00 ATOM 65 C LEU 61 70.643 34.582 86.875 1.00 1.00 ATOM 66 O LEU 61 71.104 34.312 85.763 1.00 1.00 ATOM 67 CG LEU 61 66.784 34.265 87.410 1.00 1.00 ATOM 68 CD1 LEU 61 65.740 35.374 87.433 1.00 1.00 ATOM 69 CD2 LEU 61 66.423 33.217 86.364 1.00 1.00 ATOM 71 N SER 62 71.228 35.437 87.708 1.00 1.52 ATOM 70 CA SER 62 72.478 36.102 87.360 1.00 1.52 ATOM 73 CB SER 62 72.911 37.043 88.488 1.00 1.52 ATOM 74 C SER 62 73.575 35.073 87.106 1.00 1.52 ATOM 75 O SER 62 74.353 35.206 86.159 1.00 1.52 ATOM 76 OG SER 62 71.819 37.837 88.921 1.00 1.52 ATOM 78 N GLU 63 73.623 34.040 87.939 1.00 2.73 ATOM 77 CA GLU 63 74.617 32.985 87.773 1.00 2.73 ATOM 80 CB GLU 63 74.511 31.962 88.908 1.00 2.73 ATOM 81 C GLU 63 74.456 32.288 86.427 1.00 2.73 ATOM 82 O GLU 63 75.446 31.964 85.767 1.00 2.73 ATOM 83 CG GLU 63 74.940 32.501 90.265 1.00 2.73 ATOM 84 CD GLU 63 75.115 31.415 91.312 1.00 2.73 ATOM 85 OE1 GLU 63 74.656 30.275 91.076 1.00 2.73 ATOM 86 OE2 GLU 63 75.718 31.697 92.372 1.00 2.73 ATOM 88 N ALA 64 73.212 32.066 86.011 1.00 2.78 ATOM 87 CA ALA 64 72.943 31.425 84.727 1.00 2.78 ATOM 90 CB ALA 64 71.483 30.985 84.658 1.00 2.78 ATOM 91 C ALA 64 73.260 32.366 83.570 1.00 2.78 ATOM 92 O ALA 64 73.609 31.918 82.474 1.00 2.78 ATOM 94 N GLY 65 73.154 33.669 83.815 1.00 2.41 ATOM 93 CA GLY 65 73.430 34.655 82.783 1.00 2.41 ATOM 96 C GLY 65 72.212 35.482 82.410 1.00 2.41 ATOM 97 O GLY 65 72.317 36.428 81.625 1.00 2.41 ATOM 99 N PHE 66 71.057 35.140 82.972 1.00 1.32 ATOM 98 CA PHE 66 69.828 35.881 82.705 1.00 1.32 ATOM 101 CB PHE 66 68.610 35.100 83.216 1.00 1.32 ATOM 102 C PHE 66 69.876 37.251 83.371 1.00 1.32 ATOM 103 O PHE 66 70.418 37.395 84.469 1.00 1.32 ATOM 104 CG PHE 66 68.371 33.802 82.490 1.00 1.32 ATOM 105 CD1 PHE 66 68.905 32.619 82.988 1.00 1.32 ATOM 106 CE1 PHE 66 68.681 31.418 82.317 1.00 1.32 ATOM 107 CZ PHE 66 67.931 31.404 81.149 1.00 1.32 ATOM 108 CD2 PHE 66 67.604 33.784 81.330 1.00 1.32 ATOM 109 CE2 PHE 66 67.382 32.582 80.662 1.00 1.32 ATOM 111 N HIS 67 69.323 38.259 82.702 1.00 1.33 ATOM 110 CA HIS 67 69.305 39.613 83.246 1.00 1.33 ATOM 113 CB HIS 67 70.277 40.512 82.473 1.00 1.33 ATOM 114 C HIS 67 67.902 40.207 83.195 1.00 1.33 ATOM 115 O HIS 67 67.417 40.578 82.124 1.00 1.33 ATOM 116 CG HIS 67 70.244 41.935 82.938 1.00 1.33 ATOM 117 ND1 HIS 67 70.874 42.348 84.091 1.00 1.33 ATOM 119 CE1 HIS 67 70.656 43.649 84.193 1.00 1.33 ATOM 120 NE2 HIS 67 69.844 44.063 83.235 1.00 1.33 ATOM 122 CD2 HIS 67 69.556 42.987 82.431 1.00 1.33 ATOM 124 N MET 68 67.253 40.318 84.350 1.00 2.40 ATOM 123 CA MET 68 65.897 40.855 84.412 1.00 2.40 ATOM 126 CB MET 68 65.413 40.907 85.864 1.00 2.40 ATOM 127 C MET 68 65.828 42.246 83.795 1.00 2.40 ATOM 128 O MET 68 66.478 43.180 84.271 1.00 2.40 ATOM 129 CG MET 68 65.990 39.801 86.736 1.00 2.40 ATOM 130 SD MET 68 65.567 38.155 86.119 1.00 2.40 ATOM 131 CE MET 68 63.794 38.174 86.329 1.00 2.40 ATOM 133 N VAL 69 65.036 42.384 82.738 1.00 3.52 ATOM 132 CA VAL 69 64.864 43.676 82.080 1.00 3.52 ATOM 135 CB VAL 69 63.868 43.564 80.903 1.00 3.52 ATOM 136 C VAL 69 64.350 44.696 83.091 1.00 3.52 ATOM 137 O VAL 69 64.895 45.796 83.209 1.00 3.52 ATOM 138 CG1 VAL 69 63.418 44.948 80.451 1.00 3.52 ATOM 139 CG2 VAL 69 64.501 42.802 79.745 1.00 3.52 ATOM 141 N ALA 70 63.296 44.331 83.816 1.00 3.15 ATOM 140 CA ALA 70 62.707 45.224 84.808 1.00 3.15 ATOM 143 CB ALA 70 62.578 46.633 84.237 1.00 3.15 ATOM 144 C ALA 70 61.340 44.713 85.252 1.00 3.15 ATOM 145 O ALA 70 60.677 43.977 84.516 1.00 3.15 ATOM 147 N CYS 71 60.910 45.112 86.446 1.00 2.15 ATOM 146 CA CYS 71 59.625 44.671 86.978 1.00 2.15 ATOM 149 CB CYS 71 59.773 44.251 88.444 1.00 2.15 ATOM 150 C CYS 71 58.576 45.771 86.863 1.00 2.15 ATOM 151 O CYS 71 58.832 46.919 87.234 1.00 2.15 ATOM 152 SG CYS 71 60.860 42.825 88.690 1.00 2.15 ATOM 154 N ASN 72 57.395 45.420 86.363 1.00 1.87 ATOM 153 CA ASN 72 56.317 46.391 86.192 1.00 1.87 ATOM 156 CB ASN 72 55.705 46.266 84.794 1.00 1.87 ATOM 157 C ASN 72 55.238 46.210 87.254 1.00 1.87 ATOM 158 O ASN 72 54.775 45.092 87.492 1.00 1.87 ATOM 159 CG ASN 72 56.731 46.447 83.691 1.00 1.87 ATOM 160 ND2 ASN 72 56.848 45.452 82.819 1.00 1.87 ATOM 163 OD1 ASN 72 57.421 47.467 83.628 1.00 1.87 ATOM 165 N SER 73 54.844 47.303 87.899 1.00 2.58 ATOM 164 CA SER 73 53.829 47.244 88.944 1.00 2.58 ATOM 167 CB SER 73 54.013 48.401 89.931 1.00 2.58 ATOM 168 C SER 73 52.423 47.291 88.356 1.00 2.58 ATOM 169 O SER 73 52.229 47.772 87.237 1.00 2.58 ATOM 170 OG SER 73 53.719 49.640 89.309 1.00 2.58 ATOM 172 N SER 74 51.442 46.803 89.109 1.00 4.38 ATOM 171 CA SER 74 50.057 46.814 88.651 1.00 4.38 ATOM 174 CB SER 74 49.286 45.642 89.266 1.00 4.38 ATOM 175 C SER 74 49.368 48.125 89.008 1.00 4.38 ATOM 176 O SER 74 49.346 48.524 90.175 1.00 4.38 ATOM 177 OG SER 74 47.933 45.656 88.840 1.00 4.38 ATOM 179 N GLY 75 48.813 48.798 88.006 1.00 5.83 ATOM 178 CA GLY 75 48.137 50.066 88.235 1.00 5.83 ATOM 181 C GLY 75 49.113 51.208 88.476 1.00 5.83 ATOM 182 O GLY 75 48.878 52.011 89.402 1.00 5.83 ATOM 183 OXT GLY 75 50.116 51.304 87.739 1.00 5.83 TER END